7UD5: Histone H3
Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome. Determined by electron microscopy at 4.25 Å resolution. Released 21 Sept 2022.
- Method
- Electron microscopy
- Resolution
- 4.25 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 17
- Atoms
- 22,713
- Mol. weight
- 414.65 kDa
- Ligands
- ZN, SAH
- Released
- 21 Sept 2022
Explore 7UD5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7UD5 contains 62 α-helices and 123 β-strands across 15 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 65-78 | 14 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 51-75 | 25 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-20 | 3 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 78 | 1 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 89-98 | 10 | |
| α-helix | 102-119 | 18 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 85 | 1 | |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 7 |
| α-helix | 51-75 | 25 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 84-93 | 10 | |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 46-72 | 27 | |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-45 | 10 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| 601 DNA (146-mer) | I | DNA | 146 | synthetic construct | |
| 601 DNA (146-mer) | J | DNA | 146 | synthetic construct | |
| cDNA FLJ56846, highly similar to Zinc finger protein HRX | K | protein | 226 | Homo sapiens | B4DIJ7 |
| WD repeat-containing protein 5 | L | protein | 335 | Homo sapiens | P61964 |
| Set1/Ash2 histone methyltransferase complex subunit ASH2 | M | protein | 534 | Homo sapiens | Q9UBL3 |
| Retinoblastoma-binding protein 5 | N | protein | 538 | Homo sapiens | Q15291 |
| Polyubiquitin-B | O | protein | 81 | Homo sapiens | P0CG47 |
| Protein dpy-30 homolog | P, Q | protein | 104 | Homo sapiens | Q9C005 |
Sequence of entity 1 (A, E), FASTA
>7UD5_1 Histone H3 (chains A, E)
MARTLQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVALFEDTNLCAIHAKRVTI
LPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7UD5_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7UD5_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>7UD5_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYT
SAK
Sequence of entity 5 (I), FASTA
>7UD5_5 601 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>7UD5_6 601 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 7 (K), FASTA
>7UD5_7 cDNA FLJ56846, highly similar to Zinc finger protein HRX (chains K)
MFRFHKPEEANEPPLNPHGSARAEVHLRKSAFDMFNFLASKHRQPPEYNPNDEEEEEVQL
KSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVI
RSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQ
KHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN
Sequence of entity 8 (L), FASTA
>7UD5_8 WD repeat-containing protein 5 (chains L)
GSATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEW
LASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSG
KCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLK
LWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQG
HTDVVISTACHPTENIIASAALENDKTIKLWKSDC
Sequence of entity 9 (M), FASTA
>7UD5_9 Set1/Ash2 histone methyltransferase complex subunit ASH2 (chains M)
MDTQAGSVDEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSG
NTYFLRKQANLKEMCLSALANLTWQSRTQDEHPKTMFSKDKDIIPFIDKYWECMTTRQRP
GKMTWPNNIVKTMSKERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQS
SAVSTSGNLNGGIAAGSSGKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEH
PFNKDGYRYILAEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERVLLALHDRAPQLKI
SDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYD
KFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTETAKSLPDTYKDKALIKF
KSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTV
SINFGPCFKYPPKDLTYRPMSDMGWGAVVEHTLADVLYHVETEVDGRRSPPWEP
Sequence of entity 10 (N), FASTA
>7UD5_10 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL
Sequence of entity 11 (O), FASTA
>7UD5_11 Polyubiquitin-B (chains O)
QGSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGC
Sequence of entity 12 (P, Q), FASTA
>7UD5_12 Protein dpy-30 homolog (chains P, Q)
GAMDPMEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRA
YLDQTVVPILLQGLAVLAKERPPNPIEFLASYLLKNKAQFEDRN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
Primary citation
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Rahman, S., Hoffmann, N.A., Worden, E.J. et al. Proc Natl Acad Sci U S A (2022) 119:e2205691119-e2205691119. DOI 10.1073/pnas.2205691119 · PubMed
Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
Browse structure collections
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